I'm Sergei Tokmakov, California attorney (Bar #279869). I help healthcare SaaS founders structure exactly this. Quick framework:
You're correct that AWS's BAA covers the infrastructure layer (S3, EC2, RDS) — but you are a separate business associate under 45 CFR 160.103, and the covered entity (the clinic) is required to have a BAA in place with you before disclosing PHI. The AWS BAA flows downstream as part of your subcontractor BAA chain, but does not substitute for your direct BAA with the customer.
Practical pre-launch checklist: (1) BAA template (your own, with reasonable liability caps), (2) Privacy Policy and Notice of Privacy Practices coverage, (3) Risk Analysis under 45 CFR 164.308(a)(1)(ii)(A), (4) breach notification SOP, (5) workforce training records, (6) access logs and audit controls. The Healthcare SaaS legal package I do flat-fee at $2,500 covers the BAA template plus the SaaS subscription agreement, privacy policy, and basic compliance documentation — happy to share more if useful.
You can also model HIPAA breach exposure here: not legal advice, but practical sequencing matters more than perfect documents on day one. Get the BAA right, get the basics in place, iterate.